Bone marrow transplantation can provide an effective cell-based strategy to enhance bone repair. However, the fate of implanted cells and the extent of their contribution to bone osteoinduction remain uncertain. To define the fate of bone marrow-derived cells and their contribution in vivo, we used a bone-specific collagen I promoter (2.3Col) driving green fluorescent protein (GFP) (2.3ColGFP) within a lentiviral vector. Prior to in vivo cell fate determination, we verified a high efficiency of lentiviral transduction in human bone marrow stromal cells (hBMSCs), without altering the proliferation or differentiation potential of these cells. We showed that the 2.3ColGFP marker responded to endogenous transcriptional regulation signals. In a mouse ossicle model, we demonstrated that the 2.3ColGFP marker is able to specifically define human bone marrow-derived stem cells that enter the osteoblast lineage in vivo. In addition, cells labeled with 2.3ColGFP with the donor origin, directly make a major contribution to bone formation. Furthermore, we also demonstrated in a calvarial defect model that a mixture of human bone marrow-derived populations, have stronger bone regenerative potential than that of hBMSCs, and an optimal dose is required for bone regeneration by the mixed populations.